The early-1990s brought a wave of intense queer activism. Film scholar Vito Russo became a visiting professor at UCSC and taught a course called Documenting Gay Activism, which inspired many students on campus. ACT UP, Queer Nation, and the Lesbian Avengers organized in-your-face protests at the Capitola Mall and other public places. A sit-in for democratic education achieved support for educational diversity at UCSC, including for what was becoming called queer studies. 1990 saw the organization of the first queer theory conference at UCSC, organized by Professor Teresa de Lauretis and other members of the UCSC Faculty Lesbian and Gay Studies Group.

The 1990s also witnessed an increase in the visibility and organizing of GLBT people of color. The Lesbians of Color Alliance (LOCA), first formed in the late-1980s, was re-founded in the 1990s, and members marched together in the Santa Cruz gay pride parade. Queers of Color became an official organization in 1995, and has become increasingly more active. Progress was also made in the acceptance of gays, lesbians, and bisexuals within students of color organizations such as MEChA and APISA. The Women of Color Research Cluster, located at Oakes College, became a vibrant center of scholarship; the annual Women of Color Film Festivals were dynamic and inspiring showcases for innovative work. CLUH reorganized with a commitment to teaching workshops that focused on the intersection of heterosexism and racism.

In 1998, Todd McGregor [Bowser] and Tchad Sanger organized the national GLBT conference "Exposed", which drew five hundred participants to UC Santa Cruz, with appearances by Margo Gomez, Annie Sprinkle, Elizabeth Birch, and Kerry Lobel. The conference was covered by 60 Minutes, and Bowser and Sanger were featured on the list of Top 100 Queer Youth to Watch Out For.

The 1990s saw more institutionalization and acceptance of gay, lesbian, and bisexual [and finally transgendered] rights and concerns at the University. GLB-themed housing began at Merrill College in 1990, and then at Oakes College in 1992. In 1990, the systemwide University of California Lesbian, Gay, Bisexual Association formed at a conference at UC Santa Barbara. In 1995, Linda [Rosewood] Hooper and Tegan Speiser organized the first Gay, Lesbian, Bisexual Alumni Reunion at UCSC.

In 1997, Deborah Abbott was hired as the first director of the GLBT Center. She provides a detailed narration here of how she has built up the Center, which is now a key resource on campus. The Center began organizing the Rainbow Graduation Ceremony in 1999, and now invites local high school and community college graduates to participate in the ceremony, as there is no other such ceremony in the region. Also in 1997, a sixteen-year battle was finally won when the University of California expanded the definition of eligible family members to include adult dependent relatives and same-sex domestic partners of UC employees. Those rights were extended still further in 1999, when UCSC permitted domestic partners to live together in Family Student Housing, and in 2002, when the UC Regents voted to extend equal retirement benefits both to same-sex domestic partners and opposite-sex domestic partners.

Only in the 1990s did transgender issues begin to become a focus of queer curriculum. In 1999,  the first transgendered student was hired in a paid position as the Transgender Programs Coordinator at the GLBT Resource Center, probably the first such position in the United States. In 1996, the 'T' was added to the Gay, Lesbian, Bisexual Concerns Committee (GLBTCC). The 'T' was also added to the GLBT Resource Center's name in the late-1990s. Also in the late- 1990s, transgendered students founded the organization Genderation X. Bisexuals also became increasingly visible and accepted. Very recently, the GLBT Resource Center has mounted an effort to include intersexed people in its outreach efforts. In the year 2000, the UCGLBTA added intersex to its name. Intersex identity and experience has been beyond the historically focused Out in the Redwoods project.

Some retrenchment in the area of GLBT civil rights took place at the national level. In 1992, Colorado passed anti-gay initiative Amendment 2 (later declared unconstitutional by the U.S. Supreme Court) and a similar anti-gay initiative was narrowly defeated in Oregon in the same time period. President Clinton introduced the infamous 'Don't Ask, Don't Tell' military policy on homosexuality in 1993. That same year, transgendered [FTM] Brandon Teena was murdered in Falls City, Nebraska. In 1996, the Defense of Marriage Act passed the U.S. Congress, and in 1998, gay college student Matthew Shepard was beaten to death in Wyoming. Clearly, the struggles for GLBT people are not over.